page_4.php

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<?php

function tpps_page_4_validate_form(array &$form, array &$form_state) {

  if ($form_state['submitted'] == '1') {
    unset($form_state['file_info'][TPPS_PAGE_4]);

    $form_values = $form_state['values'];
    $organism_number = $form_state['saved_values'][TPPS_PAGE_1]['organism']['number'];

    for ($i = 1; $i <= $organism_number; $i++) {
      $organism = $form_values["organism-$i"];

      if ($i > 1 and isset($organism['phenotype-repeat-check']) and $organism['phenotype-repeat-check'] == '1') {
        unset($form_state['values']["organism-$i"]['phenotype']);
      }
      if (isset($form_state['values']["organism-$i"]['phenotype'])) {
        tpps_validate_phenotype($form_state['values']["organism-$i"]['phenotype'], $i, $form, $form_state);
      }

      if ($i > 1 and isset($organism['genotype-repeat-check']) and $organism['genotype-repeat-check'] == '1') {
        unset($form_state['values']["organism-$i"]['genotype']);
      }
      if (isset($form_state['values']["organism-$i"]['genotype'])) {
        tpps_validate_genotype($form_state['values']["organism-$i"]['genotype'], $i, $form, $form_state);
      }

      if ($i > 1 and isset($organism['environment-repeat-check']) and $organism['environment-repeat-check'] == '1') {
        unset($form_state['values']["organism-$i"]['environment']);
      }
      if (isset($form_state['values']["organism-$i"]['environment'])) {
        tpps_validate_environment($form_state['values']["organism-$i"]['environment'], "organism-$i");
      }
    }

    if (form_get_errors() and !$form_state['rebuild']) {
      $form_state['rebuild'] = TRUE;
      $new_form = drupal_rebuild_form('tpps_main', $form_state, $form);

      for ($i = 1; $i <= $organism_number; $i++) {

        if (isset($new_form["organism-$i"]['phenotype']['metadata']['upload'])) {
          $form["organism-$i"]['phenotype']['metadata']['upload'] = $new_form["organism-$i"]['phenotype']['metadata']['upload'];
          $form["organism-$i"]['phenotype']['metadata']['upload']['#id'] = "edit-organism-$i-phenotype-metadata-upload";
        }
        if (isset($new_form["organism-$i"]['phenotype']['metadata']['columns'])) {
          $form["organism-$i"]['phenotype']['metadata']['columns'] = $new_form["organism-$i"]['phenotype']['metadata']['columns'];
          $form["organism-$i"]['phenotype']['metadata']['columns']['#id'] = "edit-organism-$i-phenotype-metadata-columns";
        }

        if (isset($form["organism-$i"]['phenotype']['file'])) {
          $form["organism-$i"]['phenotype']['file']['upload'] = $new_form["organism-$i"]['phenotype']['file']['upload'];
          $form["organism-$i"]['phenotype']['file']['columns'] = $new_form["organism-$i"]['phenotype']['file']['columns'];
          $form["organism-$i"]['phenotype']['file']['upload']['#id'] = "edit-organism-$i-phenotype-file-upload";
          $form["organism-$i"]['phenotype']['file']['columns']['#id'] = "edit-organism-$i-phenotype-file-columns";
        }

        $file_types = array(
          'snps-assay',
          'other',
        );

        $field_types = array(
          'upload',
          'columns',
        );

        foreach ($file_types as $type) {
          foreach ($field_types as $field) {
            if (isset($form["organism-$i"]['genotype']['files'][$type][$field]) and isset($new_form["organism-$i"]['genotype']['files'][$type][$field])) {
              $form["organism-$i"]['genotype']['files'][$type][$field] = $new_form["organism-$i"]['genotype']['files'][$type][$field];
              $form["organism-$i"]['genotype']['files'][$type][$field]['#id'] = "edit-organism-$i-genotype-files-{$type}-{$field}";
            }
          }
        }
      }
    }
  }
}

function tpps_validate_phenotype(array $phenotype, $org_num, array $form, array &$form_state) {
  $normal_check = $phenotype['normal-check'];
  $iso_check = $phenotype['iso-check'];
  $id = "organism-$org_num";
  $thirdpage = $form_state['saved_values'][TPPS_PAGE_3];

  if (empty($normal_check) and empty($iso_check)) {
    form_set_error("$id][phenotype][normal-check", t("Please choose at least one category of phenotypes to upload"));
  }

  if ($normal_check) {
    $phenotype_number = $phenotype['phenotypes-meta']['number'];
    $phenotype_check = $phenotype['check'];
    $phenotype_meta = $phenotype['metadata'];
    $phenotype_file = $phenotype['file'];

    if ($phenotype_check == '1' and empty($phenotype_meta)) {
      form_set_error("$id][phenotype][metadata", t("Phenotype Metadata File: field is required."));
    }
    if ($phenotype_check == '1' and !empty($phenotype_meta)) {
      $required_groups = array(
        'Phenotype Id' => array(
          'id' => array(1),
        ),
        'Attribute' => array(
          'attr' => array(2),
        ),
        'Description' => array(
          'desc' => array(3),
        ),
        'Units' => array(
          'units' => array(4),
        ),
        'Structure' => array(
          'structure' => array(5),
        ),
      );

      $file_element = $form[$id]['phenotype']['metadata'];
      $groups = tpps_file_validate_columns($form_state, $required_groups, $file_element);
      if (!form_get_errors()) {
        // Get phenotype name column.
        $phenotype_name_col = $groups['Phenotype Id']['1'];

        // Preserve file if it is valid.
        tpps_preserve_valid_file($form_state, $form_state['values'][$id]['phenotype']['metadata'], $org_num, "Phenotype_Metadata");
      }
    }

    for ($i = 1; $i <= $phenotype_number; $i++) {
      $current_phenotype = $phenotype['phenotypes-meta']["$i"];
      $name = $current_phenotype['name'];
      $description = $current_phenotype['description'];
      $units = $current_phenotype['units'];

      if ($name == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][name", "Phenotype $i Name: field is required.");
      }

      if (!$current_phenotype['attribute']) {
        form_set_error("$id][phenotype][phenotypes-meta][$i][attribute", "Phenotype $i Attribute: field is required.");
      }

      if ($current_phenotype['attribute'] == 'other' and $current_phenotype['attr-other'] == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][attr-other", "Phenotype $i Custom Attribute: field is required.");
      }

      if ($description == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][description", "Phenotype $i Description: field is required.");
      }

      if ($units == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][units", "Phenotype $i Units: field is required.");
      }
      elseif ($units == 'other' and $current_phenotype['unit-other'] == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][unit-other", "Phenotype $i Custom Unit: field is required.");
      }

      if ($current_phenotype['structure'] == 'other' and $current_phenotype['struct-other'] == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][struct-other", "Phenotype $i Custom Structure: field is required.");
      }

      if (($current_phenotype['val-check'] or $current_phenotype['bin-check'] or $current_phenotype['units'] == tpps_load_cvterm('boolean')->cvterm_id) and $current_phenotype['min'] == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][min", "Phenotype $i Minimum Value: field is required.");
      }

      if (($current_phenotype['val-check'] or $current_phenotype['bin-check'] or $current_phenotype['units'] == tpps_load_cvterm('boolean')->cvterm_id) and $current_phenotype['max'] == '') {
        form_set_error("$id][phenotype][phenotypes-meta][$i][max", "Phenotype $i Maximum Value: field is required.");
      }
    }

    if ($phenotype['time']['time-check']) {
      foreach ($phenotype['time']['time_phenotypes'] as $key => $val) {
        if (!$val) {
          unset($form_state['values'][$id]['phenotype']['time']['time_phenotypes'][$key]);
          unset($form_state['values'][$id]['phenotype']['time']['time_values'][$key]);
        }
      }
      if (empty($form_state['values'][$id]['phenotype']['time']['time_phenotypes'])) {
        form_set_error("$id][phenotype][time][time_phenotypes", t("Time-based Phenotypes: field is required."));
      }
    }

    if (empty($phenotype_file)) {
      form_set_error("$id][phenotype][file", t("Phenotypes: field is required."));
    }
    if (!empty($phenotype_file)) {
      $required_groups = array(
        'Tree Identifier' => array(
          'id' => array(1),
        ),
        'Phenotype Data' => array(
          'phenotype-data' => array(0),
        ),
      );
      if ($phenotype['format'] != 0) {
        $required_groups = array(
          'Tree Identifier' => array(
            'id' => array(1),
          ),
          'Phenotype Name/Identifier' => array(
            'phenotype-name' => array(2),
          ),
          'Phenotype Value(s)' => array(
            'val' => array(3),
          ),
        );
      }

      $file_element = $form[$id]['phenotype']['file'];
      $groups = tpps_file_validate_columns($form_state, $required_groups, $file_element);

      if (!form_get_errors()) {
        $phenotype_file_tree_col = $groups['Tree Identifier']['1'];
        $phenotype_names = array();
        if ($phenotype['format'] == 0) {
          $phenotype_file_name_cols = $groups['Phenotype Data']['0'];
          $headers = tpps_file_headers($phenotype_file, !empty($phenotype['file-no-header']));
          foreach ($phenotype_file_name_cols as $column_index) {
            $phenotype_names[] = $headers[$column_index];
          }
        }
        if ($phenotype['format'] != 0) {
          $phenotype_file_name_col = $groups['Phenotype Name/Identifier']['2'];
          $phenotype_names = tpps_parse_file_column($phenotype_file, $phenotype_file_name_col);
        }

        $phenotype_meta_names = array();
        if (isset($phenotype_name_col)) {
          $phenotype_meta_names = tpps_parse_file_column($phenotype_meta, $phenotype_name_col);
        }

        for ($i = 1; $i <= $phenotype_number; $i++) {
          $phenotype_meta_names[] = $phenotype['phenotypes-meta'][$i]['name'];
        }
        $missing_phenotypes = array_diff($phenotype_names, $phenotype_meta_names);
        if (!empty($missing_phenotypes)) {
          $phenotype_id_str = implode(', ', $missing_phenotypes);
          form_set_error("$id][phenotype][file", "Phenotype file: We detected Phenotypes that were not in your Phenotype Metadata file. Please either remove these phenotypes from your Phenotype file, or add them to your Phenotype Metadata file. The phenotypes we detected with missing definitions were: $phenotype_id_str");
        }

        if (isset($phenotype_file_tree_col)) {
          $species_index = empty($thirdpage['tree-accession']['check']) ? 'species-1' : "species-$org_num";
          $tree_accession_file = $form_state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file'];
          $column_vals = $form_state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file-columns'];

          foreach ($column_vals as $col => $val) {
            if ($val == '1') {
              $id_col_accession_name = $col;
              break;
            }
          }
          $acc_no_header = $form_state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file-no-header'];
          $phenotype_no_header = $form_state['values'][$id]['phenotype']['file-no-header'];
          $missing_trees = tpps_compare_files($form_state['values'][$id]['phenotype']['file'], $tree_accession_file, $phenotype_file_tree_col, $id_col_accession_name, $phenotype_no_header, $acc_no_header);
          if ($missing_trees !== array()) {
            $tree_id_str = implode(', ', $missing_trees);
            form_set_error("$id][phenotype][file", "Phenotype file: We detected Plant Identifiers that were not in your Plant Accession file. Please either remove these plants from your Phenotype file, or add them to your Plant Accession file. The Plant Identifiers we found were: $tree_id_str");
          }
        }
      }

      // Preserve file if it is valid.
      tpps_preserve_valid_file($form_state, $form_state['values'][$id]['phenotype']['file'], $org_num, "Phenotype_Data");
    }
  }

  if ($iso_check) {
    if (empty($phenotype['iso'])) {
      form_set_error("$id][phenotype][iso", t("Phenotype Isotope/Mass Spectrometry File: field is required."));
    }

    if (!form_get_errors()) {
      $headers = tpps_file_headers($phenotype['iso']);
      $id_col_name = key($headers);
      while (($k = array_search(NULL, $headers))) {
        unset($headers[$k]);
      }
      $num_columns = tpps_file_width($phenotype['iso']) - 1;
      $num_unique_columns = count(array_unique($headers)) - 1;

      if ($num_unique_columns != $num_columns) {
        form_set_error("$id][phenotype][iso", t("Mass spectrometry/Isotope file: some columns in the file you provided are missing or have duplicate header values. Please either enter valid header values for those columns or remove those columns, then reupload your file."));
      }
    }

    if (!form_get_errors()) {
      $species_index = empty($thirdpage['tree-accession']['check']) ? 'species-1' : "species-$org_num";
      $tree_accession_file = $form_state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file'];
      $id_col_accession_name = $form_state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file-groups']['Tree Id']['1'];

      $acc_no_header = $form_state['saved_values'][TPPS_PAGE_3]['tree-accession'][$species_index]['file-no-header'];
      $missing_trees = tpps_compare_files($phenotype['iso'], $tree_accession_file, $id_col_name, $id_col_accession_name, FALSE, $acc_no_header);

      if ($missing_trees !== array()) {
        $tree_id_str = implode(', ', $missing_trees);
        form_set_error("$id][phenotype][iso", "Mass spectrometry/Isotope file: We detected Plant Identifiers that were not in your Plant Accession file. Please either remove these plants from your file, or add them to your Plant Accession file. The Plant Identifiers we found were: $tree_id_str");
      }
    }

    // Preserve file if it is valid.
    tpps_preserve_valid_file($form_state, $phenotype['iso'], $org_num, "Phenotype_Data");
  }
}

function tpps_validate_genotype(array $genotype, $org_num, array $form, array &$form_state) {
  $id = "organism-$org_num";
  $snps = $genotype['SNPs'];
  $ref_genome = $genotype['ref-genome'];
  $file_type = $genotype['files']['file-type'];
  $vcf = isset($genotype['files']['vcf']) ? $genotype['files']['vcf'] : 0;
  $snps_assay = isset($genotype['files']['snps-assay']) ? $genotype['files']['snps-assay'] : 0;
  $assoc_file = $genotype['files']['snps-association'] ?? 0;
  $other_file = isset($genotype['files']['other']) ? $genotype['files']['other'] : 0;
  $thirdpage = $form_state['saved_values'][TPPS_PAGE_3];
  $species_index = empty($thirdpage['tree-accession']['check']) ? 'species-1' : "species-$org_num";
  $tree_accession_file = $thirdpage['tree-accession'][$species_index]['file'];
  $id_col_accession_name = $thirdpage['tree-accession'][$species_index]['file-groups']['Tree Id']['1'];

  if (!$ref_genome) {
    form_set_error("$id][genotype][ref-genome", t("Reference Genome: field is required."));
  }
  elseif ($ref_genome === 'bio') {
    if (!$genotype['tripal_eutils']['accession']) {
      form_set_error("$id][genotype][tripal_eutils][accession", t('NCBI Accession Number: field is required.'));
    }
    $connection = new \EUtils();
    try {
      $connection->setPreview();
      $parsed = $connection->get($genotype['tripal_eutils']['db'], $genotype['tripal_eutils']['accession']);
      foreach ($_SESSION['messages']['status'] as $key => $message) {
        if ($message == '<pre>biosample</pre>') {
          unset($_SESSION['messages']['status'][$key]);
          if (empty($_SESSION['messages']['status'])) {
            unset($_SESSION['messages']['status']);
          }
          break;
        }
      }
      $form_state['values']['parsed'] = $parsed;
    }
    catch (\Exception $e) {
      form_set_error("$id][genotype][tripal_eutils][accession", $e->getMessage());
    }
  }
  elseif ($ref_genome === 'url' or $ref_genome === 'manual' or $ref_genome === 'manual2') {

    $class = 'FASTAImporter';
    tripal_load_include_importer_class($class);
    $fasta_vals = $genotype['tripal_fasta'];

    $file_upload = isset($fasta_vals['file']['file_upload']) ? trim($fasta_vals['file']['file_upload']) : 0;
    $file_existing = isset($fasta_vals['file']['file_upload_existing']) ? trim($fasta_vals['file']['file_upload_existing']) : 0;
    $file_remote = isset($fasta_vals['file']['file_remote']) ? trim($fasta_vals['file']['file_remote']) : 0;
    $db_id = trim($fasta_vals['db']['db_id']);
    $re_accession = trim($fasta_vals['db']['re_accession']);
    $analysis_id = trim($fasta_vals['analysis_id']);
    $seqtype = trim($fasta_vals['seqtype']);

    if (!$file_upload and !$file_existing and !$file_remote) {
      form_set_error("$id][genotype][tripal_fasta][file", t("Assembly file: field is required."));
    }

    if ($db_id and !$re_accession) {
      form_set_error("$id][genotype][tripal_fasta][additional][re_accession", t('Accession regular expression: field is required.'));
    }
    if ($re_accession and !$db_id) {
      form_set_error("$id][genotype][tripal_fasta][additional][db_id", t('External Database: field is required.'));
    }

    if (!$analysis_id) {
      form_set_error("$id][genotype][tripal_fasta][analysis_id", t('Analysis: field is required.'));
    }
    if (!$seqtype) {
      form_set_error("$id][genotype][tripal_fasta][seqtype", t('Sequence Type: field is required.'));
    }

    if (!form_get_errors()) {
      $assembly = $file_existing ? $file_existing : ($file_upload ? $file_upload : $file_remote);
    }
  }

  if (implode('', $genotype['marker-type']) === '000') {
    form_set_error("$id][genotype][marker-type", t("Genotype Marker Type: field is required."));
  }
  elseif ($genotype['marker-type']['SNPs']) {
    if (!$snps['genotyping-design']) {
      form_set_error("$id][genotype][SNPs][genotyping-design", t("Genotyping Design: field is required."));
    }
    elseif ($snps['genotyping-design'] == '1') {
      if (!$snps['GBS']) {
        form_set_error("$id][genotype][SNPs][GBS", t("GBS Type: field is required."));
      }
      elseif ($snps['GBS'] == '5' and !$snps['GBS-other']) {
        form_set_error("$id][genotype][SNPs][GBS=other", t("Custom GBS Type: field is required."));
      }
    }
    elseif ($snps['genotyping-design'] == '2') {
      if (!$snps['targeted-capture']) {
        form_set_error("$id][genotype][SNPs][targeted-capture", t("Targeted Capture: field is required."));
      }
      elseif ($snps['targeted-capture'] == '2' and !$snps['targeted-capture-other']) {
        form_set_error("$id][genotype][SNPs][targeted-capture-other", t("Custom Targeted Capture: field is required."));
      }
    }
  }
  elseif ($genotype['marker-type']['SSRs/cpSSRs'] and empty($genotype['SSRs/cpSSRs'])) {
    form_set_error("$id][genotype][SSRs/cpSSRs", t("SSRs/cpSSRs: field is required."));
  }
  elseif ($genotype['marker-type']['SSRs/cpSSRs'] and empty($genotype['files']['ploidy'])) {
    form_set_error("$id][genotype][files][ploidy", t("Ploidy: field is required."));
  }
  elseif ($genotype['marker-type']['Other'] and empty($genotype['other-marker'])) {
    form_set_error("$id][genotype][other-marker", t("Other Genotype marker: field is required."));
  }

  if (preg_match('/^0+$/', implode('', $file_type))) {
    form_set_error("$id][genotype][files][file-type", t("Genotype File Type: field is required."));
    return;
  }
  $loaded_state = tpps_load_submission($form_state['accession']);
  //$vcf = '';
  if (!empty($loaded_state['vcf_replace'])) {
    foreach ($loaded_state['vcf_replace'] as $org_num => $fid) {
      if (file_load($fid)) {
        $form_state['values']["organism-$org_num"]['genotype']['files']['vcf'] = $fid;
        $vcf = $fid;
        $form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf_check'] = NULL;
        $form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf'] = NULL;
      }
      if (!file_load($fid)) {
        form_set_error("$org_num][genotype][files][local_vcf", t("Local VCF File: File could not be loaded properly."));
      }
    }
  }

  if (!empty($file_type['VCF']) and !$vcf and trim($form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf']) == '') {
    form_set_error("$id][genotype][files][vcf", t("Genotype VCF File: field is required."));
  }
  elseif (!empty($file_type['VCF'])) {
    if (($ref_genome === 'manual' or $ref_genome === 'manual2' or $ref_genome === 'url') and isset($assembly) and $assembly and !form_get_errors()) {
      if (trim($form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf']) != '') {
        $local_vcf_path = trim($form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf']);
        $vcf_content = gzopen($local_vcf_path, 'r');
      }
      else {
        $vcf_content = gzopen(file_load($vcf)->uri, 'r');
      }
      $assembly_content = gzopen(file_load($assembly)->uri, 'r');

      while (($vcf_line = gzgets($vcf_content)) !== FALSE) {
        if ($vcf_line[0] != '#') {

          $vcf_values = explode("\t", $vcf_line);
          $scaffold_id = $vcf_values[0];
          $match = FALSE;

          while (($assembly_line = gzgets($assembly_content)) !== FALSE) {
            if ($assembly_line[0] != '>') {
              continue;
            }
            if (preg_match('/^(.*?)\s.*$/', $assembly_line, $matches)) {
              $assembly_scaffold = $matches[1];
            }
            if ($assembly_scaffold[0] == '>') {
              $assembly_scaffold = substr($assembly_scaffold, 1);
            }
            if ($assembly_scaffold == $scaffold_id) {
              $match = TRUE;
              break;
            }
          }
          if (!$match) {
            fclose($assembly_content);
            $assembly_content = gzopen(file_load($assembly)->uri, 'r');
            while (($assembly_line = gzgets($assembly_content)) !== FALSE) {
              if ($assembly_line[0] != '>') {
                continue;
              }
              if (preg_match('/^(.*?)\s.*$/', $assembly_line, $matches)) {
                $assembly_scaffold = $matches[1];
              }
              if ($assembly_scaffold[0] == '>') {
                $assembly_scaffold = substr($assembly_scaffold, 1);
              }
              if ($assembly_scaffold == $scaffold_id) {
                $match = TRUE;
                break;
              }
            }
          }

          if (!$match) {
            form_set_error("$id][genotype][files][vcf", t("VCF File: scaffold @scaffold_id not found in assembly file(s)", array('@scaffold_id' => $scaffold_id)));
          }
        }
      }

    }
    if (empty($loaded_state['vcf_replace']) && trim($form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf']) != '') {
      form_set_error("$org_num][genotype][files][local_vcf", t("Local VCF File: File needs to be pre-validated. Please click on Pre-validate my VCF files button at the bottom."));
    }
    
    if (!empty($loaded_state['vcf_validated']) and $loaded_state['vcf_validated'] === TRUE and empty($loaded_state['vcf_val_errors'])) {
      drupal_set_message(t('VCF files pre-validated. Skipping VCF file validation'));
    }
    elseif (!form_get_errors()) {
      $accession_ids = tpps_parse_file_column($tree_accession_file, $id_col_accession_name);
      $vcf_file = file_load($vcf);
      if (trim($form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf']) != '') {
        $location = trim($form_state['values']["organism-$org_num"]['genotype']['files']['local_vcf']);
      }
      else {
        $location = tpps_get_location($vcf_file->uri);
      }
      $vcf_content = gzopen($location, 'r');
      $stocks = array();
      while (($vcf_line = gzgets($vcf_content)) !== FALSE) {
        if (preg_match('/#CHROM/', $vcf_line)) {
          $vcf_line = explode("\t", $vcf_line);
          for ($j = 9; $j < count($vcf_line); $j++) {
            $stocks[] = trim($vcf_line[$j]);
          }
          break;
        }
      }

      if (count($stocks) == 0) {
        form_set_error("$id][genotype][files][vcf", t("Genotype VCF File: unable to parse Plant Identifiers. The format of your VCF file must be invalid"));
      }

      if (count($stocks) != 0) {
        $missing_plants = array();
        foreach ($stocks as $stock_id) {
          if (array_search($stock_id, $accession_ids) === FALSE) {
            $missing_plants[] = $stock_id;
          }
        }
        if (count($missing_plants) > 0) {
          $missing_plants = implode(', ', $missing_plants);
          form_set_error("$id][genotype][files][vcf", t("Genotype VCF File: We found Plant Identifiers in your VCF file that were not present in your accession file. Please either add these plants to your accession file or remove them from your VCF file. The missing plants are: @missing_plants.", array('@missing_plants' => $missing_plants)));
        }
      }

      if (!form_get_errors()) {
        $form_state['values'][$id]['genotype']['files']['vcf_genotype_count'] = tpps_file_len($vcf);
      }
    }

    // Preserve file if it is valid.
    tpps_preserve_valid_file($form_state, $vcf, $org_num, "Genotype_VCF");
  }

  if (!empty($file_type['SNPs Genotype Assay']) and !$snps_assay) {
    form_set_error("$id][genotype][files][snps-assay", t("SNPs Assay file: field is required."));
  }
  elseif (!empty($file_type['SNPs Genotype Assay'])) {
    $headers = tpps_file_headers($snps_assay);
    $id_col_name = key($headers);
    while (($k = array_search(NULL, $headers))) {
      drupal_set_message(t('Following header column is Null which needs to be fixed. %data', array('%data' => $k)), 'error');
      unset($headers[$k]);
    }
    $num_columns = tpps_file_width($snps_assay) - 1;
    $num_unique_columns = count(array_unique($headers)) - 1;
    if ($num_unique_columns != $num_columns) {
      $duplicates = array_diff_assoc($headers, array_unique($headers));
      if (!empty($duplicates)) {
        drupal_set_message(t('Following header values are duplicate in provided snp file. %data', array('%data' => implode(',', $duplicates))), 'error');
      }
      form_set_error("$id][genotype][files][snps-assay", t("SNPs Assay file: some columns in the file you provided are missing or have duplicate header values. Please either enter valid header values for those columns or remove those columns, then reupload your file."));
    }

    if (!form_get_errors()) {
      $acc_no_header = $thirdpage['tree-accession'][$species_index]['file-no-header'];
      $missing_trees = tpps_compare_files($snps_assay, $tree_accession_file, $id_col_name, $id_col_accession_name, FALSE, $acc_no_header);
      if ($missing_trees !== array()) {
        $tree_id_str = implode(', ', $missing_trees);
        form_set_error("$id][genotype][files][snps-assay", t("SNPs Assay file: We detected Plant Identifiers that were not in your Plant Accession file. Please either remove these plants from your Genotype file, or add them to your Plant Accession file. The Plant Identifiers we found were: @tree_id_str", array('@tree_id_str' => $tree_id_str)));
      }
    }

    // Preserve file if it is valid.
    tpps_preserve_valid_file($form_state, $snps_assay, $org_num, "Genotype_SNPs_Assay");

    if (!form_get_errors()) {
      if (!empty($file_type['SNPs Associations']) and !$assoc_file) {
        form_set_error("$id][genotype][files][snps-association", t("SNPs Associations file: field is required."));
      }
      elseif (!empty($file_type['SNPs Associations'])) {
        $required_groups = array(
          'SNP ID' => array(
            'id' => array(1),
          ),
          'Scaffold' => array(
            'scaffold' => array(2),
          ),
          'Position' => array(
            'position' => array(3),
          ),
          'Allele' => array(
            'allele' => array(4),
          ),
          'Associated Trait' => array(
            'trait' => array(5),
          ),
          'Confidence Value' => array(
            'confidence' => array(6),
          ),
        );

        $file_element = $form[$id]['genotype']['files']['snps-association'];
        $groups = tpps_file_validate_columns($form_state, $required_groups, $file_element);

        if (!form_get_errors()) {
          // Check that SNP IDs match Genotype Assay.
          $snps_id_col = $groups['SNP ID'][1];
          $assoc_no_header = $genotype['files']['snps-association-no-header'] ?? FALSE;

          $assay_snps = tpps_file_headers($snps_assay);
          unset($assay_snps[key($assay_snps)]);
          $assoc_snps = tpps_parse_file_column($assoc_file, $snps_id_col, $assoc_no_header);
          $missing_snps = array_diff($assoc_snps, $assay_snps);

          if ($missing_snps !== array()) {
            $snps_id_str = implode(', ', $missing_snps);
            form_set_error("$id][genotype][files][snps-association", t("SNPs Association File: We detected SNP IDs that were not in your Genotype Assay. Please either remove these SNPs from your Association file, or add them to your Genotype Assay. The SNP Identifiers we found were: @snps_id_str", array('@snps_id_str' => $snps_id_str)));
          }

          // Check that Phenotype names match phenotype metadata section.
          $trait_id_col = $groups['Associated Trait'][5];
          $association_phenotypes = tpps_parse_file_column($assoc_file, $trait_id_col, $assoc_no_header);

          $phenotype = $form_state['values'][$id]['phenotype'];
          $phenotype_meta = $phenotype['metadata'];
          $phenotype_number = $phenotype['phenotypes-meta']['number'];

          $phenotype_meta_names = array();
          $phenotype_name_col = $form_state['values'][$id]['phenotype']['metadata-groups']['Phenotype Id']['1'] ?? NULL;
          if (isset($phenotype_name_col)) {
            $phenotype_meta_names = tpps_parse_file_column($phenotype_meta, $phenotype_name_col);
          }

          for ($i = 1; $i <= $phenotype_number; $i++) {
            $phenotype_meta_names[] = $phenotype['phenotypes-meta'][$i]['name'];
          }

          $missing_phenotypes = array_diff($association_phenotypes, $phenotype_meta_names);
          if ($missing_phenotypes !== array()) {
            $phenotype_names_str = implode(', ', $missing_phenotypes);
            form_set_error("$id][genotype][files][snps-association", "SNPs Association File: We detected Associated Traits that were not specified in the Phenotype Metadata Section. Please either remove these Traits from your Association file, or add them to your Phenotype Metadata section. The Trait names we foud were: $phenotype_names_str");
          }

          // Check that position values are correctly formatted.
          $position_col = $groups['Position'][3];
          $positions = tpps_parse_file_column($assoc_file, $position_col, $assoc_no_header);
          foreach ($positions as $position) {
            if (!preg_match('/^(\d+):(\d+)$/', $position)) {
              form_set_error("$id][genotype][files][snps-association", t('SNPs Association File: We detected SNP positions that do not match the required format. The correct format is: "start:stop".'));
              break;
            }
          }
        }

        // Preserve file if it is valid.
        tpps_preserve_valid_file($form_state, $assoc_file, $org_num, "SNPs_Association");

        if (empty($genotype['files']['snps-association-type'])) {
          form_set_error("$id][genotype][files][snps-association-type", t("SNPs Association Type: field is required."));
        }

        if (empty($genotype['files']['snps-association-tool'])) {
          form_set_error("$id][genotype][files][snps-association-tool", t("SNPs Association Tool: field is required."));
        }

        if (!empty($genotype['files']['snps-pop-struct'])) {
          // Preserve file if it is valid.
          tpps_preserve_valid_file($form_state, $genotype['files']['snps-pop-struct'], $org_num, "SNPs_Population_Structure");
        }

        if (!empty($genotype['files']['snps-kinship'])) {
          // Preserve file if it is valid.
          tpps_preserve_valid_file($form_state, $genotype['files']['snps-kinship'], $org_num, "SNPs_Kinship");
        }
      }
    }
  }

  if (!empty($file_type['Assay Design']) and !$genotype['files']['assay-load']) {
    form_set_error("$id][genotype][files][assay-load", t("Assay Design: field is required."));
  }
  elseif (!empty($file_type['Assay Design']) and $genotype['files']['assay-load'] == 'new' and !$genotype['files']['assay-design']) {
    form_set_error("$id][genotype][files][assay-design", t("Assay Design file: field is required."));
  }
  elseif (!empty($file_type['Assay Design']) and $genotype['files']['assay-load'] == 'new') {
    // Preserve file if it is valid.
    tpps_preserve_valid_file($form_state, $genotype['files']['assay-design'], $org_num, "Genotype_Assay_Design");
  }
  elseif (!empty($file_type['Assay Design']) and $genotype['files']['assay-load'] != 'new') {
    $file = file_load($genotype['files']['assay-load']);
    file_usage_add($file, 'tpps', 'tpps_project', substr($form_state['accession'], 4));
    $form_state['file_info'][TPPS_PAGE_4][$file->fid] = '#NO_RENAME';
  }

  if (!empty($file_type['SSRs/cpSSRs Genotype Spreadsheet']) and !$genotype['files']['ssrs']) {
    form_set_error("$id][genotype][files][ssrs]", t("SSRs/cpSSRs Spreadsheet: field is required."));
  }
  elseif (!empty($file_type['SSRs/cpSSRs Genotype Spreadsheet']) and !empty($genotype['files']['ploidy'])) {
    $headers = tpps_file_headers($genotype['files']['ssrs']);
    $form_state['values']["organism-$org_num"]['genotype']['files']['ssrs-empty'] = $form["organism-$org_num"]['genotype']['files']['ssrs']['#value']['empty'];
    $genotype['files']['ssrs-empty'] = $form_state['values']["organism-$org_num"]['genotype']['files']['ssrs-empty'];
    $id_col_name = key($headers);
    while (($k = array_search(NULL, $headers))) {
      unset($headers[$k]);
    }
    $num_columns = tpps_file_width($genotype['files']['ssrs']) - 1;
    $num_unique_columns = count(array_unique($headers)) - 1;

    tpps_ssr_valid_ploidy($genotype['files']['ploidy'], $num_columns, $num_unique_columns, "$id][genotype][files][ssrs");

    if (!empty($genotype['files']['ssr-extra-check'])) {
      if (empty($genotype['files']['extra-ssr-type'])) {
        form_set_error("$id][genotype][files][extra-ssr-type", t("Define Additional SSRs/cpSSRs Type: field is required."));
      }

      if (!$genotype['files']['ssrs_extra']) {
        form_set_error("$id][genotype][files][ssrs_extra]", t("SSRs/cpSSRs Additional Spreadsheet: field is required."));
      }
      elseif (!empty($genotype['files']['extra-ploidy'])) {
        $headers = tpps_file_headers($genotype['files']['ssrs_extra']);
        $id_col_name = key($headers);
        while (($k = array_search(NULL, $headers))) {
          unset($headers[$k]);
        }
        $num_columns = tpps_file_width($genotype['files']['ssrs_extra']) - 1;
        $num_unique_columns = count(array_unique($headers)) - 1;

        tpps_ssr_valid_ploidy($genotype['files']['extra-ploidy'], $num_columns, $num_unique_columns, "$id][genotype][files][ssrs_extra");
      }
    }

    if (!form_get_errors()) {
      $acc_no_header = $thirdpage['tree-accession'][$species_index]['file-no-header'];
      $missing_trees = tpps_compare_files($genotype['files']['ssrs'], $tree_accession_file, $id_col_name, $id_col_accession_name, FALSE, $acc_no_header);

      if ($missing_trees !== array()) {
        $tree_id_str = implode(', ', $missing_trees);
        form_set_error("$id][genotype][files][ssrs", t("SSRs/cpSSRs Genotype Spreadsheet: We detected Plant Identifiers that were not in your Plant Accession file. Please either remove these plants from your Genotype file, or add them to your Plant Accession file. The Plant Identifiers we found were: @tree_id_str", array('@tree_id_str' => $tree_id_str)));
      }
    }

    if (!form_get_errors()) {
      $options = array(
        'empty' => $genotype['files']['ssrs-empty'] ?? NULL,
        'org_num' => $org_num,
      );
      tpps_file_iterator($genotype['files']['ssrs'], 'tpps_ssr_valid_values', $options);
    }

    // Preserve file if it is valid.
    tpps_preserve_valid_file($form_state, $genotype['files']['ssrs'], $org_num, "Genotype_SSR_Spreadsheet");
    if (!empty($genotype['files']['ssrs_extra'])) {
      tpps_preserve_valid_file($form_state, $genotype['files']['ssrs_extra'], $org_num, "Genotype_SSR_Additional_Spreadsheet");
    }
  }

  if (!empty($file_type['Indel Genotype Spreadsheet']) and !$genotype['files']['indels']) {
    form_set_error("$id][genotype][files][indels]", t("Indel Genotype Spreadsheet: field is required."));
  }
  elseif (!empty($file_type['Indel Genotype Spreadsheet'])) {
    $indel_fid = $genotype['files']['indels'];
    $headers = tpps_file_headers($indel_fid);
    $id_col_name = key($headers);
    while (($k = array_search(NULL, $headers))) {
      unset($headers[$k]);
    }
    $num_columns = tpps_file_width($indel_fid) - 1;
    $num_unique_columns = count(array_unique($headers)) - 1;

    if ($num_unique_columns != $num_columns) {
      form_set_error("$id][genotype][files][indels", t("Indel Genotype Spreadsheet: some columns in the file you provided are missing or have duplicate header values. Please either enter valid header values for those columns or remove those columns, then reupload your file."));
    }

    if (!form_get_errors()) {
      $acc_no_header = $thirdpage['tree-accession'][$species_index]['file-no-header'];
      $missing_trees = tpps_compare_files($indel_fid, $tree_accession_file, $id_col_name, $id_col_accession_name, FALSE, $acc_no_header);

      if ($missing_trees !== array()) {
        $tree_id_str = implode(', ', $missing_trees);
        form_set_error("$id][genotype][files][indels", t("Indel Genotype Spreadsheet: We detected Plant Identifiers that were not in your Plant Accession file. Please either remove these plants from your Genotype file, or add them to your Plant Accession file. The Plant Identifiers we found were: @tree_id_str", array('@tree_id_str' => $tree_id_str)));
      }
    }

    // Preserve file if it is valid.
    tpps_preserve_valid_file($form_state, $indel_fid, $org_num, "Genotype_Indel_Assay");
  }

  if (!empty($file_type['Other Marker Genotype Spreadsheet']) and !$genotype['files']['other']) {
    form_set_error("$id][genotype][files][other]", t("Other Marker Spreadsheet: field is required."));
  }
  elseif (!empty($file_type['Other Marker Genotype Spreadsheet'])) {
    if (array_key_exists('columns', $form[$id]['genotype']['files']['other'])) {
      $required_groups = array(
        'Tree Id' => array(
          'id' => array(1),
        ),
        'Genotype Data' => array(
          'data' => array(0),
        ),
      );

      $file_element = $form[$id]['genotype']['files']['other'];
      $groups = tpps_file_validate_columns($form_state, $required_groups, $file_element);
      // Get Plant Id column name.
      if (!form_get_errors()) {
        $id_col_genotype_name = $groups['Tree Id']['1'];
      }
    }
    if (!array_key_exists('columns', $form[$id]['genotype']['files']['other'])) {
      $headers = tpps_file_headers($genotype['files']['other']);
      if (!form_get_errors()) {
        $id_col_genotype_name = key($headers);
      }
    }

    if (!form_get_errors()) {
      $acc_no_header = $thirdpage['tree-accession'][$species_index]['file-no-header'];
      $other_no_header = $genotype['files']['other-no-header'] ?? FALSE;
      $missing_trees = tpps_compare_files($other_file, $tree_accession_file, $id_col_genotype_name, $id_col_accession_name, $other_no_header, $acc_no_header);

      if ($missing_trees !== array()) {
        $tree_id_str = implode(', ', $missing_trees);
        form_set_error("$id][genotype][files][other", "Other Marker Genotype Spreadsheet: We detected Plant Identifiers that were not in your Plant Accession file. Please either remove these plants from your Genotype file, or add them to your Plant Accession file. The Plant Identifiers we found were: $tree_id_str");
      }
    }

    // Preserve file if it is valid.
    tpps_preserve_valid_file($form_state, $other_file, $org_num, "Genotype_Other_Marker_Spreadsheet");
  }
}

function tpps_validate_environment(array &$environment, $id) {
  // Using cartograplant environment layers.
  $group_check = FALSE;
  $new_layers = array();
  foreach ($environment['env_layers_groups'] as $group_name => $group_id) {
    if (!empty($group_id)) {
      $group_check = TRUE;
      if ($group_name == 'WorldClim v.2 (WorldClim)') {
        $subgroups_query = db_select('cartogratree_layers', 'l')
          ->distinct()
          ->fields('l', array('subgroup_id'))
          ->condition('group_id', $group_id)
          ->execute();
        while (($subgroup = $subgroups_query->fetchObject())) {
          $subgroup_title = db_select('cartogratree_subgroups', 's')
            ->fields('s', array('subgroup_name'))
            ->condition('subgroup_id', $subgroup->subgroup_id)
            ->execute()
            ->fetchObject()->subgroup_name;
          if (!empty($environment['env_layers'][$subgroup_title])) {
            $new_layers[$subgroup_title] = $environment['env_layers'][$subgroup_title];
          }
        }
      }
      if ($group_name != 'WorldClim v.2 (WorldClim)') {
        $layer_query = db_select('cartogratree_layers', 'l')
          ->fields('l', array('title'))
          ->condition('group_id', $group_id)
          ->execute();
        while (($layer = $layer_query->fetchObject())) {
          if (!empty($environment['env_layers'][$layer->title])) {
            $new_layers[$layer->title] = $environment['env_layers'][$layer->title];
          }
        }
      }
    }
  }

  if (!empty($environment['env_layers']['other'])) {
    if (empty($environment['env_layers']['other_db'])) {
      form_set_error("$id][environment][env_layers][other_db", t('CartograPlant other environmental layer DB: field is required.'));
    }

    if (empty($environment['env_layers']['other_name'])) {
      form_set_error("$id][environment][env_layers][other_name", t('CartograPlant other environmental layer name: field is required.'));
    }

    if (empty($environment['env_layers']['other_params'])) {
      form_set_error("$id][environment][env_layers][other_params", t('CartograPlant other environmental layer parameters: field is required.'));
    }

    if (!form_get_errors()) {
      $new_layers['other'] = 'other';
      $new_layers['other_db'] = $environment['env_layers']['other_db'];
      $new_layers['other_name'] = $environment['env_layers']['other_name'];
    }
  }

  $environment['env_layers'] = $new_layers;

  if (!$group_check) {
    form_set_error("$id][environment][env_layers_groups", t('CartograPlant environmental layers groups: field is required.'));
  }
  elseif (empty($new_layers)) {
    form_set_error("$id][environment][env_layers", t('CartograPlant environmental layers: field is required.'));
  }
}

function tpps_ssr_valid_values($row, array &$options) {
  $id = array_shift($row);
  foreach ($row as $value) {
    if ($value < 0 and $value !== $options['empty']) {
      form_set_error("{$options['org_num']}-genotype-files-ssrs-{$id}", "SSRs Spreadsheet file: Some non-empty values are negative for plant \"{$id}\".");
      break;
    }
  }
}

function tpps_ssr_valid_ploidy($ploidy, $num_columns, $num_unique_columns, $name) {
  switch ($ploidy) {
    case 'Haploid':
      if ($num_unique_columns != $num_columns) {
        form_set_error($name, t("SSRs/cpSSRs Genotype Spreadsheet: some columns in the file you provided are missing or have duplicate header values. Please either enter header values for those columns or remove those columns, then reupload your file."));
      }
      break;

    case 'Diploid':
      if ($num_unique_columns != $num_columns and $num_columns / $num_unique_columns !== 2) {
        form_set_error($name, t("SSRs/cpSSRs Genotype Spreadsheet: There is either an invalid number of columns in your file, or some of your columns are missing values. Please review and reupload your file."));
      }
      elseif ($num_unique_columns == $num_columns and $num_columns % 2 !== 0) {
        form_set_error($name, t("SSRs/cpSSRs Genotype Spreadsheet: There is either an invalid number of columns in your file, or some of your columns are missing values. Please review and reupload your file."));
      }
      break;

    case 'Polyploid':
      if ($num_columns % $num_unique_columns !== 0) {
        form_set_error($name, t("SSRs/cpSSRs Genotype Spreadsheet: There is either an invalid number of columns in your file, or some of your columns are missing values. Please review and reupload your file."));
      }
      break;

    default:
      break;
  }
}